Contacts of the helix formed by residues 48 - 58 (chain B) in PDB entry 5W5T
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 48 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B VAL* 4.3 11.9 - - + -
20B ALA* 3.7 30.3 - - + -
37B PRO* 2.9 23.8 + - + +
46B ARG* 4.7 1.3 - - + -
47B ILE* 1.3 75.7 - - - +
49B ASP* 1.3 75.2 + - - +
50B PHE 3.1 1.9 + - - -
51B ALA* 3.4 4.7 + - - +
52B LEU* 3.3 32.3 + - + +
65B VAL* 3.9 15.7 - - + -
74B LEU* 3.9 25.6 - - + -
77B HIS* 4.1 11.7 - - + -
78B LEU* 4.5 6.5 - - + -
135B GLY* 3.5 16.2 - - - +
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ALA* 4.2 1.8 - - + -
46B ARG 2.9 27.6 + - - +
47B ILE 2.9 1.0 + - - -
48B ILE* 1.3 77.5 - - - +
50B PHE* 1.3 56.6 + - + +
52B LEU* 4.5 0.2 - - - -
53B SER* 2.5 37.2 + - - -
77B HIS* 2.7 28.5 + - - -
82B TRP* 3.2 18.5 + - - -
300B ILE* 3.7 10.8 - - + +
301B TRP 3.4 15.7 - - - +
302B THR* 2.6 27.7 + - - -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.9 28.7 - + - -
45B ALA* 4.6 8.7 - - + -
46B ARG 4.0 11.7 - - - -
47B ILE* 3.1 18.3 + - - +
48B ILE 3.1 0.8 - - - -
49B ASP* 1.3 78.0 - - - +
51B ALA* 1.3 61.1 + - - +
53B SER* 3.2 4.5 + - - -
54B ASN* 2.8 37.2 + - - +
137B HIS 4.1 10.5 - - - +
138B ILE* 3.8 30.7 - - + -
139B TYR* 3.8 21.8 - - + +
140B LYS* 4.7 5.6 - - + -
291B LEU* 4.5 13.2 - - + -
293B ILE* 6.4 0.7 - - + -
300B ILE* 3.8 37.9 - - + +
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B VAL* 4.7 8.9 - - + +
47B ILE 4.5 0.4 + - - -
48B ILE 3.4 8.0 + - - +
50B PHE* 1.3 77.6 - - - +
52B LEU* 1.3 58.3 + - - +
54B ASN* 3.4 12.4 + - - +
55B ALA* 3.0 27.5 + - - +
133B LEU* 4.0 15.2 - - + +
134B ALA 4.0 20.2 - - - +
135B GLY* 4.6 9.2 - - - -
137B HIS 4.9 3.5 + - - +
139B TYR* 4.3 12.5 - - + +
143B TYR* 3.9 3.7 + - - -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.0 11.2 - - + -
48B ILE* 3.3 28.6 + - + +
50B PHE 3.2 0.4 - - - -
51B ALA* 1.3 76.9 - - - +
53B SER* 1.3 58.1 + - - +
55B ALA* 3.4 6.5 + - - +
56B LEU* 3.0 27.5 + - - +
63B ILE* 3.7 33.0 - - + +
65B VAL* 3.8 15.7 - - + -
78B LEU* 3.7 23.1 - - + -
82B TRP* 3.4 48.2 - - + +
93B PHE* 3.8 7.0 - - + -
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ASP 2.5 24.3 + - - -
50B PHE 3.7 2.5 - - - -
52B LEU* 1.3 75.3 - - - +
54B ASN* 1.3 59.5 + - - +
56B LEU* 4.3 4.7 - - - -
57B ASN* 2.8 38.4 + - - +
82B TRP* 3.8 7.9 - - - -
299B PRO 3.7 19.3 - - - -
300B ILE* 3.5 12.7 - - - -
301B TRP* 2.9 27.5 + - - -
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Residues in contact with ASN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PHE 2.8 23.6 + - - +
51B ALA 3.5 1.3 - - - +
52B LEU 3.3 0.2 - - - -
53B SER* 1.3 73.3 - - - +
55B ALA* 1.3 55.4 + - - +
57B ASN 3.8 0.3 - - - -
58B SER* 2.7 37.4 + - - -
139B TYR* 3.0 39.9 + - - +
140B LYS* 3.3 6.9 - - - +
141B MET 3.2 19.9 + - - +
143B TYR* 3.2 31.3 + - + +
298B TRP* 3.1 24.2 + - - +
300B ILE* 5.2 1.2 - - - +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ALA* 3.8 29.2 - - + -
18B VAL* 6.1 0.2 - - + -
51B ALA 3.0 17.0 + - - +
52B LEU* 3.7 6.1 - - - +
53B SER 3.3 0.2 - - - -
54B ASN* 1.3 77.6 - - - +
56B LEU* 1.3 60.2 + - - +
58B SER* 3.4 3.3 + - - -
59B GLY 3.4 0.2 + - - -
60B ILE* 2.9 35.8 + - + +
63B ILE* 4.1 13.5 - - + -
133B LEU* 4.6 1.1 - - + -
143B TYR* 3.4 14.5 - - + -
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LEU 3.0 17.3 + - - +
53B SER* 3.7 4.9 - - - +
55B ALA* 1.3 75.3 - - - +
57B ASN* 1.3 68.6 + - - +
59B GLY* 3.0 20.3 + - - -
60B ILE 4.0 8.4 - - - +
63B ILE* 4.8 2.3 - - + +
82B TRP* 4.2 20.0 - - + -
84B PHE* 4.1 18.4 - - + -
85B PHE* 4.0 27.8 - - + -
299B PRO 6.0 0.4 - - - +
301B TRP* 4.6 11.4 - - + -
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Residues in contact with ASN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B SER* 2.8 23.3 + - - +
56B LEU* 1.3 85.4 - - - +
58B SER* 1.3 59.7 + - - +
59B GLY* 3.4 0.5 + - - -
298B TRP* 3.4 49.9 - - + -
299B PRO* 2.8 53.3 + - - +
12D ARG* 4.1 10.2 + - - -
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA* 3.4 15.9 - - - +
54B ASN 2.7 21.2 + - - -
55B ALA* 3.8 5.2 - - - -
56B LEU 3.2 0.6 - - - -
57B ASN* 1.3 76.7 - - - +
59B GLY* 1.3 57.5 + - - +
60B ILE* 3.5 4.9 - - - -
141B MET 3.6 1.6 + - - -
142B ASP* 3.5 11.7 - - - -
143B TYR* 2.9 41.9 + - - -
144B GLU* 4.3 3.7 - - - +
298B TRP* 3.6 2.9 - - - -
9D PRO* 5.8 0.7 - - - +
12D ARG* 3.1 23.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il